Hi Eugene,
I cannot speak for a whaler, but the length of sailing warships generally included only the hull, not the appendages. There was the length of the gun deck, length of the keel, length of the load line, length between perpendiculars. From what I could research the 106 feet 11 inches is the length on the upper deck between the rabbet at the stem and the rabbet at the stern post. If I remember correctly it was usually measured to the inside of the rabbet, but at times the outside of the rabbet. Hopefully a member with more knowledge can clarify this. I am pretty sure the Hillman, Jethro and Zachariah drawings of the Charles Morgan have a scale so that should make things a bit easier.
Allan